TY - CHAP
T1 - Chip-SIP
T2 - Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS
AU - Mayali, Xavier
AU - Weber, Peter K.
AU - Nuccio, Erin
AU - Lietard, Jory
AU - Somoza, Mark
AU - Blazewicz, Steven J.
AU - Pett-Ridge, Jennifer
N1 - Publisher Copyright:
© Springer Science+Business Media, LLC, part of Springer Nature 2019.
PY - 2019
Y1 - 2019
N2 - Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes (13C, 15N, and 18O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.
AB - Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes (13C, 15N, and 18O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.
KW - 16S rRNA
KW - C
KW - Microarrays
KW - Microbial ecology
KW - N
KW - NanoSIMS
KW - O
KW - Stable isotope probing
UR - https://www.scopus.com/pages/publications/85071473799
U2 - 10.1007/978-1-4939-9721-3_6
DO - 10.1007/978-1-4939-9721-3_6
M3 - Chapter
C2 - 31407297
AN - SCOPUS:85071473799
T3 - Methods in Molecular Biology
SP - 71
EP - 87
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -